From c7b976e4fbb0168e46f60df1e2111fdb29aa0640 Mon Sep 17 00:00:00 2001
From: Adam Fekete <adam@fekete.co.uk>
Date: Fri, 2 Dec 2022 23:09:02 +0000
Subject: [PATCH] Resolve "minor fixes for the pipeline" * removing `env.js`
from the repository * removing `matid` dependency form the parser packages *
converting python dependency check job into manual job
---
.dockerignore | 11 +-
.gitignore | 9 +-
.gitlab-ci.yml | 11 +-
Dockerfile | 6 +-
MANIFEST.in | 3 +-
dependencies/matid | 2 +-
dependencies/parsers/electronic | 2 +-
docs/develop/setup.md | 9 +-
gui/.vscode/settings.json | 19 -
gui/src/components/conftest.spec.js | 2 +-
gui/src/metainfo.json | 523 +++++++++++++++-------
gui/src/parserMetadata.json | 4 +-
gui/src/setupTests.js | 2 +-
gui/{public => tests}/env.js | 2 +-
gui/tests/{nomad-test.yaml => nomad.yaml} | 0
pyproject.toml | 2 -
requirements-dev.txt | 17 +-
requirements.txt | 17 +-
scripts/build_sdist.sh | 1 -
scripts/check_gui_artifacts.sh | 5 +-
scripts/generate_gui_artifacts.sh | 3 +-
scripts/generate_gui_config.sh | 10 +
22 files changed, 435 insertions(+), 225 deletions(-)
delete mode 100644 gui/.vscode/settings.json
rename gui/{public => tests}/env.js (99%)
rename gui/tests/{nomad-test.yaml => nomad.yaml} (100%)
create mode 100755 scripts/generate_gui_config.sh
diff --git a/.dockerignore b/.dockerignore
index 4559fa0445..85508f56ad 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -10,9 +10,6 @@ dependencies/**/tests
dependencies/**/regtests
dependencies/parsers/phonopy-library/example*
-# Ignore storage folders of docker-compose
-**/.volumes
-
# ==============================================================================
# The following part was geneterated based on the .gitignore
@@ -34,7 +31,8 @@ gui/junit.xml
# Ignore all user-specific configuration files
**/nomad.yaml
-!tests/nomad.yaml
+gui/public/env.js
+!gui/tests/nomad.yaml
!ops/docker-compose/nomad-oasis/configs/nomad.yaml
!ops/docker-compose/nomad-oasis-with-keycloak/configs/nomad.yaml
@@ -52,7 +50,12 @@ examples/workdir/
**/jupyterhub.sqlite
**/jupyterhub-proxy.pid
+# Ignore storage folders of docker-compose
+**/.volumes
+# local folder
+local
+tmp
# https://github.com/github/gitignore/blob/main/Python.gitignore
diff --git a/.gitignore b/.gitignore
index 9ea5937418..5859277c48 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,7 +16,8 @@ gui/junit.xml
# Ignore all user-specific configuration files
nomad.yaml
-!tests/nomad.yaml
+gui/public/env.js
+!gui/tests/nomad.yaml
!ops/docker-compose/nomad-oasis/configs/nomad.yaml
!ops/docker-compose/nomad-oasis-with-keycloak/configs/nomad.yaml
@@ -38,6 +39,10 @@ jupyterhub-proxy.pid
# Ignore storage folders of docker-compose
.volumes
+# local folder
+local
+tmp
+
# https://github.com/github/gitignore/blob/main/Python.gitignore
@@ -428,5 +433,3 @@ $RECYCLE.BIN/
# .nfs files are created when an open file is removed but is still being accessed
.nfs*
-# local folder
-local
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 657c974346..a696a5f9ac 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -110,7 +110,7 @@ check python dependencies:
rules:
- if: $CI_COMMIT_TAG
when: never
- - when: on_success
+ - when: manual
allow_failure: true
@@ -123,6 +123,12 @@ check gui artifacts:
- cd /app
script:
- scripts/check_gui_artifacts.sh
+ after_script:
+ - >
+ if [ $CI_JOB_STATUS == 'failed' ]; then
+ echo 'Make sure that the right GUI artifacts have been regenerated and committed by running'
+ echo './scripts/generate_gui_artifacts.sh'
+ fi
rules:
- if: $CI_COMMIT_TAG
when: never
@@ -170,8 +176,9 @@ gui tests:
image: ${CI_REGISTRY_IMAGE}/dev_node:${DOCKER_TAG}
variables:
GIT_STRATEGY: none
- script:
+ before_script:
- cd /app/gui
+ script:
- yarn test --ci --collectCoverage --reporters=default --reporters=jest-junit --silent
--testPathIgnorePatterns=MetainfoBrowser.spec.js
--testPathIgnorePatterns=src/components/entry/ArchiveEntryView.spec.js
diff --git a/Dockerfile b/Dockerfile
index eaa86aa527..3a7d4a690f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -109,22 +109,24 @@ COPY .pylintrc \
# Files requiered for artifact generation/testing
COPY ops/docker-compose ./ops/docker-compose
+
COPY gui/src/metainfo.json ./gui/src/metainfo.json
COPY gui/src/searchQuantities.json ./gui/src/searchQuantities.json
COPY gui/src/toolkitMetadata.json ./gui/src/toolkitMetadata.json
COPY gui/src/unitsData.js ./gui/src/unitsData.js
COPY gui/src/parserMetadata.json ./gui/src/parserMetadata.json
-COPY gui/public/env.js ./gui/public/env.js
COPY dependencies/nomad-remote-tools-hub/tools.json ./dependencies/nomad-remote-tools-hub/tools.json
COPY gui/src/northTools.json ./gui/src/northTools.json
COPY gui/src/exampleUploads.json ./gui/src/exampleUploads.json
+COPY gui/tests/nomad.yaml ./gui/tests/nomad.yaml
+COPY gui/tests/env.js ./gui/tests/env.js
+
# build the example upload files
RUN ./scripts/generate_example_uploads.sh
# Copy the built gui code
COPY --from=dev_node /app/gui/build nomad/app/static/gui
-RUN rm nomad/app/static/gui/env.js
# Build documentation
RUN --mount=source=.git,target=.git,type=bind pip install ".[parsing,infrastructure,dev]"
diff --git a/MANIFEST.in b/MANIFEST.in
index bba6e4815b..ecc6cecf72 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,10 +1,11 @@
prune *
exclude *
+recursive-include nomad *.py *.json *.j2 *.md *.txt metadata.yaml
include pyproject.toml setup.py AUTHORS LICENSE README.md README.parsers.md requirements.txt requirements-dev.txt
-recursive-include nomad *.py *.json *.j2 *.md *.txt metadata.yaml
graft nomad/app/static
+exclude nomad/app/static/gui/env.js
recursive-exclude nomad/app/static *.map
include dependencies/matid/README.md
diff --git a/dependencies/matid b/dependencies/matid
index c97f285949..f0c363777c 160000
--- a/dependencies/matid
+++ b/dependencies/matid
@@ -1 +1 @@
-Subproject commit c97f2859492265a46651fc0ca9f908db30b40911
+Subproject commit f0c363777c03948a08effbbe96e04a73121833ea
diff --git a/dependencies/parsers/electronic b/dependencies/parsers/electronic
index 74134f826a..74a2e6b243 160000
--- a/dependencies/parsers/electronic
+++ b/dependencies/parsers/electronic
@@ -1 +1 @@
-Subproject commit 74134f826a4508220424c52fc8bcbc8c392630d4
+Subproject commit 74a2e6b24389c8f364b9c378613a442b004c9af0
diff --git a/docs/develop/setup.md b/docs/develop/setup.md
index f6a84870a8..b419ea20a0 100644
--- a/docs/develop/setup.md
+++ b/docs/develop/setup.md
@@ -243,9 +243,14 @@ To run the worker directly with celery, do (from the root)
celery -A nomad.processing worker -l info
```
-Before you can run the gui, make sure that generated artifacts have been created:
+Before you can run the gui, make sure that generated artifacts are up-to-date:
```sh
-./generate_gui_artifacts.sh
+./scripts/generate_gui_artifacts.sh
+```
+
+Also, make sure that the config file (`gui/public/env.js`) have been properly created:
+```sh
+./scripts/generate_gui_config.sh
```
If you run the gui on its own (e.g. with react dev server below), you also have to have
diff --git a/gui/.vscode/settings.json b/gui/.vscode/settings.json
deleted file mode 100644
index 3a86e53cf5..0000000000
--- a/gui/.vscode/settings.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "editor.rulers": [
- 90
- ],
- "editor.renderWhitespace": "all",
- "editor.tabSize": 4,
- "files.trimTrailingWhitespace": true,
- "[javascript]": {
- "editor.tabSize": 2
- },
- "files.exclude": {
- "**/node_modules": true
- },
- "files.watcherExclude": {
- "**": true,
- "**/**": true
- },
- "jest.autoRun": "off"
-}
diff --git a/gui/src/components/conftest.spec.js b/gui/src/components/conftest.spec.js
index 35637c3bda..a355790a4d 100644
--- a/gui/src/components/conftest.spec.js
+++ b/gui/src/components/conftest.spec.js
@@ -325,7 +325,7 @@ let filepath
const responseCapture = {}
const readMode = process.env.READ_MODE || 'snapshot'
const writeMode = process.env.WRITE_MODE || 'none'
-const configPath = 'gui/tests/nomad-test.yaml'
+const configPath = 'gui/tests/nomad.yaml'
if (!fs.existsSync(`../${configPath}`)) {
throw Error(`
Could not find the NOMAD config file for testing at ../${configPath}. Note
diff --git a/gui/src/metainfo.json b/gui/src/metainfo.json
index 46f50c6f1d..d13e94b3e1 100644
--- a/gui/src/metainfo.json
+++ b/gui/src/metainfo.json
@@ -156,7 +156,7 @@
"name": "HubbardModel",
"description": "Setup of the Hubbard model used in DFT+U",
"extending_sections": [
- "/packages/37/section_definitions/25"
+ "/packages/37/section_definitions/26"
],
"quantities": [
{
@@ -259,7 +259,7 @@
"description": "Contains method-related information about a kind of atom identified by label. This allows the assignment of an atom-centered basis set or pseudopotential for different\natoms belonging to the same kind.",
"extending_sections": [
"/packages/28/section_definitions/6",
- "/packages/37/section_definitions/24",
+ "/packages/37/section_definitions/25",
"/packages/45/section_definitions/65",
"/packages/48/section_definitions/11",
"/packages/14/section_definitions/8",
@@ -1113,6 +1113,9 @@
"m_parent_sub_section": "section_definitions",
"name": "GW",
"description": "Section containing the various parameters that define a GW calculation.",
+ "extending_sections": [
+ "/packages/36/section_definitions/9"
+ ],
"quantities": [
{
"m_def": "nomad.metainfo.metainfo.Quantity",
@@ -1826,8 +1829,8 @@
"/packages/12/section_definitions/3",
"/packages/34/section_definitions/2",
"/packages/35/section_definitions/5",
- "/packages/36/section_definitions/14",
- "/packages/37/section_definitions/21",
+ "/packages/36/section_definitions/15",
+ "/packages/37/section_definitions/22",
"/packages/38/section_definitions/6",
"/packages/39/section_definitions/29",
"/packages/40/section_definitions/2",
@@ -2751,8 +2754,8 @@
"/packages/33/section_definitions/21",
"/packages/12/section_definitions/0",
"/packages/34/section_definitions/5",
- "/packages/36/section_definitions/10",
- "/packages/37/section_definitions/23",
+ "/packages/36/section_definitions/11",
+ "/packages/37/section_definitions/24",
"/packages/38/section_definitions/4",
"/packages/39/section_definitions/24",
"/packages/42/section_definitions/11",
@@ -4374,7 +4377,7 @@
"description": "This section stores information on a band structure evaluation along one-dimensional pathways in the $k$ or $q$ (reciprocal) space given in section_band_segment.\nEigenvalues calculated at the actual $k$-mesh used for energy_total evaluations,\ncan be found in the eigenvalues section.",
"extending_sections": [
"/packages/29/section_definitions/53",
- "/packages/37/section_definitions/20",
+ "/packages/37/section_definitions/21",
"/packages/45/section_definitions/63"
],
"quantities": [
@@ -4519,6 +4522,9 @@
"base_sections": [
"/packages/2/section_definitions/1"
],
+ "extending_sections": [
+ "/packages/37/section_definitions/20"
+ ],
"quantities": [
{
"m_def": "nomad.metainfo.metainfo.Quantity",
@@ -5924,7 +5930,7 @@
"extending_sections": [
"/packages/12/section_definitions/1",
"/packages/34/section_definitions/3",
- "/packages/36/section_definitions/13",
+ "/packages/36/section_definitions/14",
"/packages/37/section_definitions/19",
"/packages/38/section_definitions/5",
"/packages/39/section_definitions/27",
@@ -5951,7 +5957,7 @@
"/packages/33/section_definitions/22",
"/packages/34/section_definitions/8",
"/packages/35/section_definitions/8",
- "/packages/36/section_definitions/9",
+ "/packages/36/section_definitions/10",
"/packages/37/section_definitions/18",
"/packages/39/section_definitions/25",
"/packages/40/section_definitions/1",
@@ -6279,8 +6285,8 @@
"/packages/32/section_definitions/330",
"/packages/33/section_definitions/19",
"/packages/12/section_definitions/2",
- "/packages/36/section_definitions/15",
- "/packages/37/section_definitions/22",
+ "/packages/36/section_definitions/16",
+ "/packages/37/section_definitions/23",
"/packages/38/section_definitions/3",
"/packages/39/section_definitions/26",
"/packages/42/section_definitions/7",
@@ -288649,6 +288655,180 @@
"m_def": "nomad.metainfo.metainfo.Section",
"m_parent_index": 9,
"m_parent_sub_section": "section_definitions",
+ "name": "GW",
+ "base_sections": [
+ "/packages/0/section_definitions/15"
+ ],
+ "extends_base_section": true,
+ "quantities": [
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 0,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_frequency_number",
+ "description": "Number referring to the frequency used in the calculation of the self energy.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "int32"
+ },
+ "shape": [
+ "n_frequencies"
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 1,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_frequency_weights",
+ "description": "Weights of the frequency used in the calculation of the self energy.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [
+ "n_frequencies"
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 2,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_frequency_grid_type",
+ "description": "Frequency integration grid type for the correlational self energy: 'eqdis' -\nequidistant frequencies from 0 to freqmax; 'gaulag' - Gauss-Laguerre quadrature\nfrom 0 to infinity; 'gauleg' - Gauss-Legendre quadrature from 0 to freqmax;\n'gaule2' (default) - double Gauss-Legendre quadrature from 0 to freqmax and from\nfreqmax to infinity.",
+ "type": {
+ "type_kind": "python",
+ "type_data": "str"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 3,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_max_frequency",
+ "description": "Maximum frequency for the calculation of the self energy.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 4,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_bare_coulomb_cutofftype",
+ "description": "Cutoff type for the calculation of the bare Coulomb potential: none, 0d, 1d, 2d.\nSee Rozzi et al., PRB 73, 205119 (2006)",
+ "type": {
+ "type_kind": "python",
+ "type_data": "str"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 5,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_bare_coulomb_gmax",
+ "description": "Maximum G for the pw basis for the Coulomb potential.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "1 / meter"
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 6,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_mixed_basis_gmax",
+ "description": "Cut-off parameter for the truncation of the expansion of the plane waves in the\ninterstitial region.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "1 / meter"
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 7,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_mixed_basis_lmax",
+ "description": "Maximum l value used for the radial functions within the muffin-tin.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "int32"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 8,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_mixed_basis_tolerance",
+ "description": "Eigenvalue threshold below which the egenvectors are discarded in the construction\nof the radial basis set.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 9,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_self_energy_c_number_of_poles",
+ "description": "Number of poles used in the analytical continuation.",
+ "type": {
+ "type_kind": "python",
+ "type_data": "int"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 10,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_self_energy_singularity_treatment",
+ "description": "Treatment of the integrable singular terms in the calculation of the self energy.\nValues: 'mpb' - Auxiliary function method by S. Massidda, M. Posternak, and A.\nBaldereschi, PRB 48, 5058 (1993); 'crg' - Auxiliary function method by P. Carrier,\nS. Rohra, and A. Goerling, PRB 75, 205126 (2007).",
+ "type": {
+ "type_kind": "python",
+ "type_data": "str"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 11,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_screened_coulomb_volume_average",
+ "description": "Type of volume averaging for the dynamically screened Coulomb potential: isotropic\n- Simple averaging along a specified direction using only diagonal components of\nthe dielectric tensor; anisotropic - Anisotropic screening by C. Freysoldt et al.,\nCPC 176, 1-13 (2007)",
+ "type": {
+ "type_kind": "python",
+ "type_data": "str"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 12,
+ "m_parent_sub_section": "quantities",
+ "name": "x_exciting_qp_equation_treatment",
+ "description": "Methods to solve the quasi-particle equation: 'linearization', 'self-consistent'",
+ "type": {
+ "type_kind": "python",
+ "type_data": "str"
+ },
+ "shape": []
+ }
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 10,
+ "m_parent_sub_section": "section_definitions",
"name": "Calculation",
"base_sections": [
"/packages/2/section_definitions/34"
@@ -289663,7 +289843,7 @@
"m_parent_index": 3,
"m_parent_sub_section": "sub_sections",
"name": "x_exciting_section_MT_charge_atom",
- "sub_section": "/packages/36/section_definitions/11",
+ "sub_section": "/packages/36/section_definitions/12",
"repeats": true
},
{
@@ -289671,14 +289851,14 @@
"m_parent_index": 4,
"m_parent_sub_section": "sub_sections",
"name": "x_exciting_section_MT_moment_atom",
- "sub_section": "/packages/36/section_definitions/12",
+ "sub_section": "/packages/36/section_definitions/13",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 10,
+ "m_parent_index": 11,
"m_parent_sub_section": "section_definitions",
"name": "System",
"base_sections": [
@@ -290273,7 +290453,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 11,
+ "m_parent_index": 12,
"m_parent_sub_section": "section_definitions",
"name": "x_exciting_section_MT_charge_atom",
"description": "atom-resolved charges in muffin tins",
@@ -290319,7 +290499,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 12,
+ "m_parent_index": 13,
"m_parent_sub_section": "section_definitions",
"name": "x_exciting_section_MT_moment_atom",
"description": "atom-resolved moments in muffin tins",
@@ -290367,7 +290547,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 13,
+ "m_parent_index": 14,
"m_parent_sub_section": "section_definitions",
"name": "ScfIteration",
"base_sections": [
@@ -290765,7 +290945,7 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_exciting_section_MT_charge_atom_scf_iteration",
- "sub_section": "/packages/36/section_definitions/11",
+ "sub_section": "/packages/36/section_definitions/12",
"repeats": true
},
{
@@ -290773,14 +290953,14 @@
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "x_exciting_section_MT_moment_atom_scf_iteration",
- "sub_section": "/packages/36/section_definitions/12",
+ "sub_section": "/packages/36/section_definitions/13",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 14,
+ "m_parent_index": 15,
"m_parent_sub_section": "section_definitions",
"name": "Method",
"base_sections": [
@@ -291466,7 +291646,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 15,
+ "m_parent_index": 16,
"m_parent_sub_section": "section_definitions",
"name": "Run",
"base_sections": [
@@ -291927,7 +292107,7 @@
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_vdW_TS",
- "sub_section": "/packages/37/section_definitions/17",
+ "sub_section": "/packages/37/section_definitions/14",
"repeats": true
}
]
@@ -292079,23 +292259,6 @@
"m_def": "nomad.metainfo.metainfo.Section",
"m_parent_index": 4,
"m_parent_sub_section": "section_definitions",
- "name": "x_fhi_aims_section_eigenvalues_group_perturbativeGW",
- "description": "section for full list of eigenvalues for different spin and kpoints from a perturbative GW calculation",
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "x_fhi_aims_section_eigenvalues_spin_perturbativeGW",
- "sub_section": "/packages/37/section_definitions/10",
- "repeats": true
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 5,
- "m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_eigenvalues_group_ZORA",
"description": "section for full list of eigenvalues for different spin and kpoints of scaled ZORA",
"sub_sections": [
@@ -292104,14 +292267,14 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_spin_ZORA",
- "sub_section": "/packages/37/section_definitions/11",
+ "sub_section": "/packages/37/section_definitions/8",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 6,
+ "m_parent_index": 5,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_eigenvalues_group",
"description": "section for full list of eigenvalues for different spin and kpoints",
@@ -292121,100 +292284,14 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_spin",
- "sub_section": "/packages/37/section_definitions/12",
+ "sub_section": "/packages/37/section_definitions/9",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 7,
- "m_parent_sub_section": "section_definitions",
- "name": "x_fhi_aims_section_eigenvalues_list_perturbativeGW",
- "description": "section for one list of eigenvalues from a perturbative GW calculation",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "x_fhi_aims_eigenvalue_correlation_perturbativeGW",
- "description": "Correlation energy at a given eigenstate from perturbative GW",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "x_fhi_aims_eigenvalue_ExactExchange_perturbativeGW",
- "description": "Exact exchange energy at given eigenstate from perturbative GW",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "x_fhi_aims_eigenvalue_ks_ExchangeCorrelation",
- "description": "KS exchange correlation energy at a given eigenstate needed to calculate the\nquasi-particle energy in perturbative GW",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "x_fhi_aims_eigenvalue_ks_GroundState",
- "description": "KS ground state energy at a given eigenstate needed in perturbative GW",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "x_fhi_aims_eigenvalue_occupation_perturbativeGW",
- "description": "Occupation of single eigenfunction of perturbative GW",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "x_fhi_aims_eigenvalue_quasiParticle_energy",
- "description": "Quasiparticle energy at a given eigenstate from perturbative GW",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 8,
+ "m_parent_index": 6,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_eigenvalues_list_ZORA",
"description": "section for one list of eigenvalues at specific kpoint and spin of scaled ZORA",
@@ -292248,7 +292325,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 9,
+ "m_parent_index": 7,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_eigenvalues_list",
"description": "section for one list of eigenvalues at specific kpoint and spin",
@@ -292282,14 +292359,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 10,
- "m_parent_sub_section": "section_definitions",
- "name": "x_fhi_aims_section_eigenvalues_spin_perturbativeGW",
- "description": "section for one spin orientation from a perturbative GW calculation"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 11,
+ "m_parent_index": 8,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_eigenvalues_spin_ZORA",
"description": "section for one spin orientation of scaled ZORA",
@@ -292337,14 +292407,14 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_list_ZORA",
- "sub_section": "/packages/37/section_definitions/8",
+ "sub_section": "/packages/37/section_definitions/6",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 12,
+ "m_parent_index": 9,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_eigenvalues_spin",
"description": "section for one spin orientation",
@@ -292392,7 +292462,7 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_list_perturbativeGW",
- "sub_section": "/packages/37/section_definitions/7",
+ "sub_section": "/packages/37/section_definitions/16",
"repeats": true
},
{
@@ -292400,14 +292470,14 @@
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_list",
- "sub_section": "/packages/37/section_definitions/9",
+ "sub_section": "/packages/37/section_definitions/7",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 13,
+ "m_parent_index": 10,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_eigenvalues_ZORA",
"description": "section for gathering eigenvalues of scaled ZORA",
@@ -292417,21 +292487,21 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_group_ZORA",
- "sub_section": "/packages/37/section_definitions/5",
+ "sub_section": "/packages/37/section_definitions/4",
"repeats": false
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 14,
+ "m_parent_index": 11,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_MD_detect",
"description": "Section to detect MD immediately during parsing of controlInOut"
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 15,
+ "m_parent_index": 12,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_parallel_task_assignement",
"description": "-",
@@ -292464,7 +292534,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 16,
+ "m_parent_index": 13,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_parallel_tasks",
"description": "-",
@@ -292474,14 +292544,14 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_parallel_task_assignement",
- "sub_section": "/packages/37/section_definitions/15",
+ "sub_section": "/packages/37/section_definitions/12",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 17,
+ "m_parent_index": 14,
"m_parent_sub_section": "section_definitions",
"name": "x_fhi_aims_section_vdW_TS",
"description": "-",
@@ -292549,6 +292619,116 @@
}
]
},
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 15,
+ "m_parent_sub_section": "section_definitions",
+ "name": "x_fhi_aims_section_eigenvalues_group_perturbativeGW",
+ "description": "section for full list of eigenvalues for different spin and kpoints from a perturbative GW calculation",
+ "sub_sections": [
+ {
+ "m_def": "nomad.metainfo.metainfo.SubSection",
+ "m_parent_index": 0,
+ "m_parent_sub_section": "sub_sections",
+ "name": "x_fhi_aims_section_eigenvalues_spin_perturbativeGW",
+ "sub_section": "/packages/37/section_definitions/17",
+ "repeats": true
+ }
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 16,
+ "m_parent_sub_section": "section_definitions",
+ "name": "x_fhi_aims_section_eigenvalues_list_perturbativeGW",
+ "description": "section for one list of eigenvalues from a perturbative GW calculation",
+ "quantities": [
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 0,
+ "m_parent_sub_section": "quantities",
+ "name": "x_fhi_aims_eigenvalue_correlation_perturbativeGW",
+ "description": "Correlation energy at a given eigenstate from perturbative GW",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "joule"
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 1,
+ "m_parent_sub_section": "quantities",
+ "name": "x_fhi_aims_eigenvalue_ExactExchange_perturbativeGW",
+ "description": "Exact exchange energy at given eigenstate from perturbative GW",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "joule"
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 2,
+ "m_parent_sub_section": "quantities",
+ "name": "x_fhi_aims_eigenvalue_ks_ExchangeCorrelation",
+ "description": "KS exchange correlation energy at a given eigenstate needed to calculate the\nquasi-particle energy in perturbative GW",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "joule"
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 3,
+ "m_parent_sub_section": "quantities",
+ "name": "x_fhi_aims_eigenvalue_ks_GroundState",
+ "description": "KS ground state energy at a given eigenstate needed in perturbative GW",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "joule"
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 4,
+ "m_parent_sub_section": "quantities",
+ "name": "x_fhi_aims_eigenvalue_occupation_perturbativeGW",
+ "description": "Occupation of single eigenfunction of perturbative GW",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 5,
+ "m_parent_sub_section": "quantities",
+ "name": "x_fhi_aims_eigenvalue_quasiParticle_energy",
+ "description": "Quasiparticle energy at a given eigenstate from perturbative GW",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "joule"
+ }
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 17,
+ "m_parent_sub_section": "section_definitions",
+ "name": "x_fhi_aims_section_eigenvalues_spin_perturbativeGW",
+ "description": "section for one spin orientation from a perturbative GW calculation"
+ },
{
"m_def": "nomad.metainfo.metainfo.Section",
"m_parent_index": 18,
@@ -292643,7 +292823,7 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_group_perturbativeGW",
- "sub_section": "/packages/37/section_definitions/4",
+ "sub_section": "/packages/37/section_definitions/15",
"repeats": false
},
{
@@ -292651,7 +292831,7 @@
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_ZORA",
- "sub_section": "/packages/37/section_definitions/13",
+ "sub_section": "/packages/37/section_definitions/10",
"repeats": false
}
]
@@ -292862,7 +293042,7 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_eigenvalues_group",
- "sub_section": "/packages/37/section_definitions/6",
+ "sub_section": "/packages/37/section_definitions/5",
"repeats": false
}
]
@@ -292871,6 +293051,31 @@
"m_def": "nomad.metainfo.metainfo.Section",
"m_parent_index": 20,
"m_parent_sub_section": "section_definitions",
+ "name": "DosValues",
+ "base_sections": [
+ "/packages/2/section_definitions/16"
+ ],
+ "extends_base_section": true,
+ "quantities": [
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 0,
+ "m_parent_sub_section": "quantities",
+ "name": "x_fhi_aims_normalization_factor_raw_data",
+ "description": "Normalization factor to reobtain the DOS values as presented in the raw data files.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "default": 1
+ }
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 21,
+ "m_parent_sub_section": "section_definitions",
"name": "BandStructure",
"base_sections": [
"/packages/2/section_definitions/14"
@@ -292941,7 +293146,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 21,
+ "m_parent_index": 22,
"m_parent_sub_section": "section_definitions",
"name": "Method",
"base_sections": [
@@ -293549,14 +293754,14 @@
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_MD_detect",
- "sub_section": "/packages/37/section_definitions/14",
+ "sub_section": "/packages/37/section_definitions/11",
"repeats": true
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 22,
+ "m_parent_index": 23,
"m_parent_sub_section": "section_definitions",
"name": "Run",
"base_sections": [
@@ -293669,14 +293874,14 @@
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "x_fhi_aims_section_parallel_tasks",
- "sub_section": "/packages/37/section_definitions/16",
+ "sub_section": "/packages/37/section_definitions/13",
"repeats": false
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 23,
+ "m_parent_index": 24,
"m_parent_sub_section": "section_definitions",
"name": "System",
"base_sections": [
@@ -293817,7 +294022,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 24,
+ "m_parent_index": 25,
"m_parent_sub_section": "section_definitions",
"name": "AtomParameters",
"base_sections": [
@@ -293837,7 +294042,7 @@
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 25,
+ "m_parent_index": 26,
"m_parent_sub_section": "section_definitions",
"name": "HubbardModel",
"base_sections": [
diff --git a/gui/src/parserMetadata.json b/gui/src/parserMetadata.json
index fe7558effc..12d90d03c4 100644
--- a/gui/src/parserMetadata.json
+++ b/gui/src/parserMetadata.json
@@ -265,10 +265,11 @@
"codeUrl": "https://aimsclub.fhi-berlin.mpg.de/",
"parserDirName": "dependencies/electronic/electronicparsers/fhi-aims/",
"parserGitUrl": "https://github.com/nomad-coe/electronic-parsers.git",
+ "parserLastUpdate": "18.10.2022",
"parserSpecific": "",
"preamble": "",
"status": "production",
- "tableOfFiles": "|Input Filename| Description|\n|--- | --- |\n|`<text_file>` | **Mainfile**, plain text file w/arbitrary name, e.g., `<output,control, aims,...>.out` |\n|`control.in` | Runtime information |\n|`geometry.in` | Material's atomic-structure information, |\n|AUX FILES| Description|\n|`<atoml_label>_l_proj_dos.out`| Angular-momentum-resolved DOS @ Fermi Energy|\n|`<atoml_label>_l_proj_dos_raw.out`| Angular-momentum-resolved DOS @ vacuum|\n|`KS_DOS_total.dat`| Kohn-Sham total DOS @ Fermi Energy |\n|`KS_DOS_total_raw.dat`| Kohn-Sham total DOS @ vacuum |\n|`Mulliken.out` **WARNING-->**|Mulliken charge analysis on all atoms. **WARNING** not yet read by NOMAD's parser|\n|`atom_proj_dos_<atom_name><index>_raw.dat` | Atom-projected DOS @ vacuum|\n|`atom_projected_dos_<atom_name><index>.dat` | Atom-projected DOS @ Fermi Energy|\n|`band<spin><segment>.out` | bandstructure file |\n"
+ "tableOfFiles": "|Input Filename| Description|\n|--- | --- |\n|`<text_file>` | **Mainfile**, plain text file w/arbitrary name, e.g., `<output,control, aims,...>.out` |\n|`control.in` | Runtime information |\n|`geometry.in` | Material's atomic-structure information, |\n|AUX FILES| Description|\n|`<atoml_label>_l_proj_dos.out`| Angular-momentum-resolved DOS @ Fermi Energy|\n|`<atoml_label>_l_proj_dos_raw.out`| Angular-momentum-resolved DOS @ vacuum|\n|`KS_DOS_total.dat`| Kohn-Sham total DOS @ Fermi Energy |\n|`KS_DOS_total_raw.dat`| Kohn-Sham total DOS @ vacuum |\n|`Mulliken.out` **WARNING-->**|Mulliken charge analysis on all atoms. **WARNING** not yet read by NOMAD's parser|\n|`atom_proj_dos_<atom_name><index>_raw.dat` | Atom-projected DOS @ vacuum|\n|`atom_projected_dos_<atom_name><index>.dat` | Atom-projected DOS @ Fermi Energy|\n|`band<spin><segment>.out` | bandstructure file |\n|`GW_band<spin><segment>` | GW bandstructure file |\n"
},
"FHI-vibes": {
"codeCategory": "Workflow manager",
@@ -742,6 +743,7 @@
"codeUrl": "http://exciting-code.org/",
"parserDirName": "dependencies/electronic/electronicparsers/exciting/",
"parserGitUrl": "https://github.com/nomad-coe/electronic-parsers.git",
+ "parserLastUpdate": "18.10.2022",
"parserSpecific": "",
"preamble": "",
"status": "production",
diff --git a/gui/src/setupTests.js b/gui/src/setupTests.js
index c769d63c0c..789bb5bf2d 100644
--- a/gui/src/setupTests.js
+++ b/gui/src/setupTests.js
@@ -20,7 +20,7 @@
import { setupServer } from 'msw/node'
import { configure } from '@testing-library/react'
-import "../public/env"
+import "../tests/env"
import '@testing-library/jest-dom' // Adds convenient expect-methods
/**
diff --git a/gui/public/env.js b/gui/tests/env.js
similarity index 99%
rename from gui/public/env.js
rename to gui/tests/env.js
index 888744463e..34bac3718d 100644
--- a/gui/public/env.js
+++ b/gui/tests/env.js
@@ -2,7 +2,7 @@ window.nomadEnv = {
"appBase": "http://localhost:8000/fairdi/nomad/latest",
"northBase": "http://localhost:9000/fairdi/nomad/latest/north",
"keycloakBase": "https://nomad-lab.eu/fairdi/keycloak/auth/",
- "keycloakRealm": "fairdi_nomad_prod",
+ "keycloakRealm": "fairdi_nomad_test",
"keycloakClientId": "nomad_public",
"debug": false,
"encyclopediaBase": "https://nomad-lab.eu/prod/rae/encyclopedia/#",
diff --git a/gui/tests/nomad-test.yaml b/gui/tests/nomad.yaml
similarity index 100%
rename from gui/tests/nomad-test.yaml
rename to gui/tests/nomad.yaml
diff --git a/pyproject.toml b/pyproject.toml
index 8499fcb02a..c82f75636c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -48,8 +48,6 @@ parsing = [
'h5py==3.6.0',
'hjson==3.0.2',
'scipy==1.7.1',
- 'scikit-learn==0.24.2',
- 'matid==0.6.1',
'python-magic==0.4.24',
'panedr==0.2',
'parmed==3.0.0',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index e305c73112..819ab47aa6 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -15,7 +15,7 @@ argon2-cffi==21.3.0 # via -r requirements.txt, jupyter-server
argon2-cffi-bindings==21.2.0 # via -r requirements.txt, argon2-cffi
arrow==1.2.3 # via -r requirements.txt, isoduration
asciitree==0.3.3 # via -r requirements.txt, zarr
-ase==3.19.0 # via -r requirements.txt, asr, matid, matid (dependencies/matid/pyproject.toml), nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml)
+ase==3.19.0 # via -r requirements.txt, asr, matid (dependencies/matid/pyproject.toml), nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml)
asr==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
astroid==2.5.1 # via nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pylint
asttokens==2.1.0 # via devtools
@@ -44,7 +44,6 @@ certipy==0.1.3 # via -r requirements.txt, jupyterhub
cffi==1.15.1 # via -r requirements.txt, argon2-cffi-bindings, bcrypt, cryptography
cftime==1.6.2 # via -r requirements.txt, netcdf4
charset-normalizer==2.0.12 # via -r requirements.txt, httpx, requests
-chronic==0.3.4 # via -r requirements.txt, matid
click==8.1.3 # via -r requirements.txt, asr, flask, mkdocs, nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pip-tools, uvicorn
cloudpickle==2.2.0 # via -r requirements.txt, dask
colorama==0.4.6 # via twine
@@ -82,7 +81,7 @@ flatdict==4.0.1 # via -r requirements.txt, nexusparser (dependencies/p
fonttools==4.37.3 # via -r requirements.txt, matplotlib
fqdn==1.5.1 # via -r requirements.txt, jsonschema
fsspec==2022.11.0 # via -r requirements.txt, dask, hyperspy
-future==0.18.2 # via -r requirements.txt, matid, uncertainties
+future==0.18.2 # via -r requirements.txt, uncertainties
ghp-import==2.1.0 # via mkdocs
gitdb==4.0.9 # via -r requirements.txt, gitpython
gitpython==3.1.24 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -137,7 +136,6 @@ m2r==0.2.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
mako==1.2.4 # via -r requirements.txt, alembic
markdown==3.4.1 # via mkdocs, mkdocs-material, pymdown-extensions
markupsafe==2.1.1 # via -r requirements.txt, jinja2, mako, nbconvert, nomad-lab (pyproject.toml), werkzeug
-matid==0.6.1 # via -r requirements.txt, electronicparsers (dependencies/parsers/electronic/pyproject.toml), nomad-lab (pyproject.toml)
matplotlib==3.5.3 # via -r requirements.txt, ase, asr, hyperspy, mdanalysis, phonopy, pymatgen
matplotlib-inline==0.1.6 # via -r requirements.txt, ipykernel, ipython
mccabe==0.6.1 # via pylint
@@ -167,12 +165,12 @@ nbconvert==7.2.5 # via -r requirements.txt, jupyter-server
nbformat==5.7.0 # via -r requirements.txt, jupyter-server, nbclient, nbconvert
nest-asyncio==1.5.6 # via -r requirements.txt, ipykernel, jupyter-client, nbclient
netcdf4==1.5.4 # via -r requirements.txt, electronicparsers (dependencies/parsers/electronic/pyproject.toml), nomad-lab (pyproject.toml)
-networkx==2.6.3 # via -r requirements.txt, matid, matid (dependencies/matid/pyproject.toml), mdanalysis, pymatgen, scikit-image
+networkx==2.6.3 # via -r requirements.txt, matid (dependencies/matid/pyproject.toml), mdanalysis, pymatgen, scikit-image
nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
numba==0.56.4 # via -r requirements.txt, hyperspy, sparse
numcodecs==0.10.2 # via -r requirements.txt, zarr
numexpr==2.8.4 # via -r requirements.txt, hyperspy
-numpy==1.21.2 # via -r requirements.txt, ase, biopython, cftime, dask, griddataformats, gsd, h5grove, h5py, hyperspy, imageio, matid, matid (dependencies/matid/pyproject.toml), matplotlib, mdanalysis, mdtraj, mrcfile, netcdf4, nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, pandas, phonopy, pymatgen, pyscf, pywavelets, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, xrdtools, zarr
+numpy==1.21.2 # via -r requirements.txt, ase, biopython, cftime, dask, griddataformats, gsd, h5grove, h5py, hyperspy, imageio, matid (dependencies/matid/pyproject.toml), matplotlib, mdanalysis, mdtraj, mrcfile, netcdf4, nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, pandas, phonopy, pymatgen, pyscf, pywavelets, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, xrdtools, zarr
oauthenticator==14.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via -r requirements.txt, jupyterhub
openpyxl==3.0.9 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -252,18 +250,17 @@ ruamel-yaml==0.17.21 # via -r requirements.txt, jupyter-telemetry, pymatgen
ruamel-yaml-clib==0.2.7 # via -r requirements.txt, ruamel-yaml
runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
scikit-image==0.19.3 # via -r requirements.txt, hyperspy
-scikit-learn==0.24.2 # via -r requirements.txt, matid (dependencies/matid/pyproject.toml), nomad-lab (pyproject.toml)
-scipy==1.7.1 # via -r requirements.txt, ase, atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), griddataformats, hyperspy, matid, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, nomad-lab (pyproject.toml), pymatgen, pyscf, scikit-image, scikit-learn, sparse
+scikit-learn==0.24.2 # via -r requirements.txt, matid (dependencies/matid/pyproject.toml)
+scipy==1.7.1 # via -r requirements.txt, ase, atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), griddataformats, hyperspy, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, nomad-lab (pyproject.toml), pymatgen, pyscf, scikit-image, scikit-learn, sparse
send2trash==1.8.0 # via -r requirements.txt, jupyter-server
sentinels==1.0.0 # via -r requirements.txt, mongomock
six==1.16.0 # via -r requirements.txt, asttokens, astunparse, basicauth, bcrypt, bleach, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, pytest, python-dateutil, python-multipart, rdflib, rfc3339-validator, validators
-sklearn==0.0.post1 # via -r requirements.txt, matid
smmap==5.0.0 # via -r requirements.txt, gitdb
sniffio==1.3.0 # via -r requirements.txt, anyio, httpcore, httpx
snowballstemmer==2.2.0 # via -r requirements.txt, sphinx
soupsieve==2.3.2.post1 # via -r requirements.txt, beautifulsoup4
sparse==0.13.0 # via -r requirements.txt, hyperspy
-spglib==2.0.2 # via -r requirements.txt, asr, matid, matid (dependencies/matid/pyproject.toml), phonopy, pymatgen
+spglib==2.0.2 # via -r requirements.txt, asr, matid (dependencies/matid/pyproject.toml), phonopy, pymatgen
sphinx==5.3.0 # via -r requirements.txt, recommonmark
sphinxcontrib-applehelp==1.0.2 # via -r requirements.txt, sphinx
sphinxcontrib-devhelp==1.0.2 # via -r requirements.txt, sphinx
diff --git a/requirements.txt b/requirements.txt
index d6990fc601..51b74dfa77 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -15,7 +15,7 @@ argon2-cffi==21.3.0 # via jupyter-server
argon2-cffi-bindings==21.2.0 # via argon2-cffi
arrow==1.2.3 # via isoduration
asciitree==0.3.3 # via zarr
-ase==3.19.0 # via asr, matid, matid (dependencies/matid/pyproject.toml), nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml)
+ase==3.19.0 # via asr, matid (dependencies/matid/pyproject.toml), nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml)
asr==0.4.1 # via nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
astunparse==1.6.3 # via mdtraj
async-generator==1.10 # via jupyterhub
@@ -40,7 +40,6 @@ certipy==0.1.3 # via jupyterhub
cffi==1.15.1 # via argon2-cffi-bindings, bcrypt, cryptography
cftime==1.6.2 # via netcdf4
charset-normalizer==2.0.12 # via httpx, requests
-chronic==0.3.4 # via matid
click==8.1.3 # via asr, flask, nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), uvicorn
cloudpickle==2.2.0 # via dask
commonmark==0.9.1 # via recommonmark
@@ -73,7 +72,7 @@ flatdict==4.0.1 # via nexusparser (dependencies/parsers/nexus/pyprojec
fonttools==4.37.3 # via matplotlib
fqdn==1.5.1 # via jsonschema
fsspec==2022.11.0 # via dask, hyperspy
-future==0.18.2 # via matid, uncertainties
+future==0.18.2 # via uncertainties
gitdb==4.0.9 # via gitpython
gitpython==3.1.24 # via nomad-lab (pyproject.toml)
greenlet==2.0.1 # via sqlalchemy
@@ -122,7 +121,6 @@ lxml==4.7.1 # via atomisticparsers (dependencies/parsers/atomistic
m2r==0.2.1 # via nomad-lab (pyproject.toml)
mako==1.2.4 # via alembic
markupsafe==2.1.1 # via jinja2, mako, nbconvert, werkzeug
-matid==0.6.1 # via electronicparsers (dependencies/parsers/electronic/pyproject.toml), nomad-lab (pyproject.toml)
matplotlib==3.5.3 # via ase, asr, hyperspy, mdanalysis, phonopy, pymatgen
matplotlib-inline==0.1.6 # via ipykernel, ipython
mdanalysis==2.1.0 # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-lab (pyproject.toml)
@@ -142,12 +140,12 @@ nbconvert==7.2.5 # via jupyter-server
nbformat==5.7.0 # via jupyter-server, nbclient, nbconvert
nest-asyncio==1.5.6 # via ipykernel, jupyter-client, nbclient
netcdf4==1.5.4 # via electronicparsers (dependencies/parsers/electronic/pyproject.toml), nomad-lab (pyproject.toml)
-networkx==2.6.3 # via matid, matid (dependencies/matid/pyproject.toml), mdanalysis, pymatgen, scikit-image
+networkx==2.6.3 # via matid (dependencies/matid/pyproject.toml), mdanalysis, pymatgen, scikit-image
nptyping==1.4.4 # via nomad-lab (pyproject.toml)
numba==0.56.4 # via hyperspy, sparse
numcodecs==0.10.2 # via zarr
numexpr==2.8.4 # via hyperspy
-numpy==1.21.2 # via ase, biopython, cftime, dask, griddataformats, gsd, h5grove, h5py, hyperspy, imageio, matid, matid (dependencies/matid/pyproject.toml), matplotlib, mdanalysis, mdtraj, mrcfile, netcdf4, nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, pandas, phonopy, pymatgen, pyscf, pywavelets, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, xrdtools, zarr
+numpy==1.21.2 # via ase, biopython, cftime, dask, griddataformats, gsd, h5grove, h5py, hyperspy, imageio, matid (dependencies/matid/pyproject.toml), matplotlib, mdanalysis, mdtraj, mrcfile, netcdf4, nexusparser (dependencies/parsers/nexus/pyproject.toml), nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, pandas, phonopy, pymatgen, pyscf, pywavelets, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, xrdtools, zarr
oauthenticator==14.2.0 # via nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via jupyterhub
openpyxl==3.0.9 # via nomad-lab (pyproject.toml)
@@ -209,18 +207,17 @@ ruamel-yaml==0.17.21 # via jupyter-telemetry, pymatgen
ruamel-yaml-clib==0.2.7 # via ruamel-yaml
runstats==2.0.0 # via nomad-lab (pyproject.toml)
scikit-image==0.19.3 # via hyperspy
-scikit-learn==0.24.2 # via matid (dependencies/matid/pyproject.toml), nomad-lab (pyproject.toml)
-scipy==1.7.1 # via ase, atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), griddataformats, hyperspy, matid, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, nomad-lab (pyproject.toml), pymatgen, pyscf, scikit-image, scikit-learn, sparse
+scikit-learn==0.24.2 # via matid (dependencies/matid/pyproject.toml)
+scipy==1.7.1 # via ase, atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), griddataformats, hyperspy, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, nomad-lab (pyproject.toml), pymatgen, pyscf, scikit-image, scikit-learn, sparse
send2trash==1.8.0 # via jupyter-server
sentinels==1.0.0 # via mongomock
six==1.16.0 # via astunparse, basicauth, bcrypt, bleach, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, python-dateutil, python-multipart, rdflib, rfc3339-validator, validators
-sklearn==0.0.post1 # via matid
smmap==5.0.0 # via gitdb
sniffio==1.3.0 # via anyio, httpcore, httpx
snowballstemmer==2.2.0 # via sphinx
soupsieve==2.3.2.post1 # via beautifulsoup4
sparse==0.13.0 # via hyperspy
-spglib==2.0.2 # via asr, matid, matid (dependencies/matid/pyproject.toml), phonopy, pymatgen
+spglib==2.0.2 # via asr, matid (dependencies/matid/pyproject.toml), phonopy, pymatgen
sphinx==5.3.0 # via recommonmark
sphinxcontrib-applehelp==1.0.2 # via sphinx
sphinxcontrib-devhelp==1.0.2 # via sphinx
diff --git a/scripts/build_sdist.sh b/scripts/build_sdist.sh
index 074d25a13e..289bccaf1a 100755
--- a/scripts/build_sdist.sh
+++ b/scripts/build_sdist.sh
@@ -21,6 +21,5 @@ yarn run build
cd ..
mkdir -p nomad/app/static/gui
cp -r build/* nomad/app/static/gui
-rm nomad/app/static/gui/env.js
python -m build --sdist
\ No newline at end of file
diff --git a/scripts/check_gui_artifacts.sh b/scripts/check_gui_artifacts.sh
index 782ff6c8ae..5eea2692c8 100755
--- a/scripts/check_gui_artifacts.sh
+++ b/scripts/check_gui_artifacts.sh
@@ -21,9 +21,8 @@ diff gui/src/unitsData.js tmp/unitsData.js
diff gui/src/exampleUploads.json tmp/exampleUploads.json
diff gui/src/northTools.json tmp/northTools.json
-python -m nomad.cli dev gui-config >tmp/env.js
-
-diff gui/public/env.js tmp/env.js
+NOMAD_CONFIG=gui/tests/nomad.yaml python -m nomad.cli dev gui-config >tmp/env.js
+diff gui/tests/env.js tmp/env.js
# cleanup
rm -rf tmp
diff --git a/scripts/generate_gui_artifacts.sh b/scripts/generate_gui_artifacts.sh
index f2a12693c3..45b22b50f0 100755
--- a/scripts/generate_gui_artifacts.sh
+++ b/scripts/generate_gui_artifacts.sh
@@ -8,4 +8,5 @@ project_dir=$(dirname $(dirname $(realpath $0)))
cd $project_dir
python -m nomad.cli dev gui-artifacts --output-directory gui/src
-python -m nomad.cli dev gui-config >gui/public/env.js
+
+NOMAD_CONFIG=gui/tests/nomad.yaml python -m nomad.cli dev gui-config >gui/tests/env.js
diff --git a/scripts/generate_gui_config.sh b/scripts/generate_gui_config.sh
new file mode 100755
index 0000000000..5e890930f0
--- /dev/null
+++ b/scripts/generate_gui_config.sh
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+set -e
+
+working_dir=$(pwd)
+project_dir=$(dirname $(dirname $(realpath $0)))
+
+cd $project_dir
+
+python -m nomad.cli dev gui-config >gui/public/env.js
--
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